South-African COVID Breakthrough sequencing

Real-time cohort building and COVID sequencing

In order to build case-control cohort we monitored all positive PCR tests in Clalit labs on the daily basis and used several covariates such as age, municipality of residence, geographical district of residence and sector to match newly infected cases in vaccinated population with unvaccinated controls.

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The usual PCR testing process does not involve storing and saving test samples, so we needed to communicate efficiently on a daily basis with the laboratories so they can prevent relevant samples from destroying and send them to the Tel Aviv University for sequencing.

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To achieve it, we built a fully automated process using combination of SQL, R, Python and Jenkins that ran every day and:

• Found relevant positive PCRs in vaccinated patients for two groups – vaccinated with only 1st dose of BNT162b2 (Pfizer) vaccine and vaccinated with 2 doses

• Used covariates from EHR data to find unvaccinated match for each of them

• Sent the lists of tests IDs to the relevant Clalit laboratories.
   

Then, Clalit Labs were able to select relevant test samples and send them to the Tel-Aviv Univesity’s Edmond J. Safra Center for Bioinformatics.

We collected data in this manner for month and our colleagues from Tel-Aviv University analyzed 813 viral genome sequence from different individuals, consisting of 149 pairs of dose2–controls, 247 pairs of dose1–controls and additional samples whose match did not undergo successful sequencing.